[gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

[Justin Lemkul]

On 5/27/17 2:44 PM, Erik Marklund wrote:
> Hi Mark,
> 
> Thinking out loud: “Non-Hbonding pairs within 3.5 Å”.
> 

I think it should be more explicit, and exactly what we always tell people:

-num:  number of hydrogen bonds as a function of time. The second column 
contains the number of atom pairs that satisfy the distance criterion but not 
the angle criterion for hydrogen bonding.

-Justin

> Kind regards,
> Erik
> 
>> On 27 May 2017, at 17:56, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>
>> Hi,
>>
>> So what should we document in the help text as the meaning, so we don't
>> keep having emails about this?
>>
>> Mark
>>
>> On Sat, May 27, 2017 at 4:36 PM Erik Marklund <erik.marklund at kemi.uu.se>
>> wrote:
>>
>>>
>>>
>>> On 26 May 2017, at 22:12, David van der Spoel <spoel at xray.bmc.uu.se
>>> <mailto:spoel at xray.bmc.uu.se>> wrote:
>>>
>>> On 26/05/17 22:05, Erik Marklund wrote:
>>> “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which
>>> is why they are sometimes fewer than the hbonds.
>>>
>>> Therefore I would assume they are more instead.
>>>
>>>
>>> They sometimes are, but not necessarily. I pointed it out because
>>> sometimes people ask if g_hbond is buggy when they see that there are
>>> occasionally lower numbers in the third column, assuming that it contains
>>> all pairs within 3.5 Å regardless of angle which should more numeorus  than
>>> the pairs that also fullfil the angle criterion. That’s not the meaning of
>>> the third column however.
>>>
>>> Kind regards,
>>> Erik
>>>
>>> On 26 May 2017, at 19:38, Adarsh V. K. <adarsh_p130085bt at nitc.ac.in
>>> <mailto:adarsh_p130085bt at nitc.ac.in>> wrote:
>>>
>>> Dear all,
>>>
>>> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "
>>>
>>> I would like to edit the file before viewing in 'Xmgrace'
>>>
>>> I opened the hbnum.xvg using 'gedit'. It shows following details (see
>>> below)
>>>
>>> Can you please tell me what is there in the third column of the file?
>>>
>>> ---------------------------------------------------------
>>> # gmx hbond is part of G R O M A C S:
>>> #
>>> # GROtesk MACabre and Sinister
>>> #
>>> @    title "Hydrogen Bonds"
>>> @    xaxis  label "Time (ps)"
>>> @    yaxis  label "Number"
>>> @TYPE xy
>>> @ view 0.15, 0.15, 0.75, 0.85
>>> @ legend on
>>> @ legend box on
>>> @ legend loctype view
>>> @ legend 0.78, 0.8
>>> @ legend length 2
>>> @ s0 legend "Hydrogen bonds"
>>> @ s1 legend "Pairs within 0.35 nm"
>>>        0            2           7
>>>       10           2           5
>>>       20           4           3
>>>       30           3           2
>>>       40           3           3
>>>       50           5           1
>>>       60           3           6
>>>       70           3           6
>>>       80           2           3
>>>       90           5           1
>>>      100          3           3
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org<mailto:
>>> gmx-users-request at gromacs.org>.
>>>
>>>
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205 <018-471%2042%2005>
>>> .
>>> http://www.icm.uu.se<http://www.icm.uu.se/>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org<mailto:
>>> gmx-users-request at gromacs.org>.
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>> -- 
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> 

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================